We are running paired-end total RNA (using blood) on HiSeq and after adapter and quality trimming (Q>30), we use tophat2 for alignment. We are getting about 90% overall mapping, but around 80% of those are mapping to multiple locations.
I am pretty sure this is way too high, but don't know what the issue is. Are there any recommendations for how we can reduce the multi-mapping or ideas on what might have caused it. Thanks!
I am pretty sure this is way too high, but don't know what the issue is. Are there any recommendations for how we can reduce the multi-mapping or ideas on what might have caused it. Thanks!
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